Using the entity metadata wrapper with a field list of references.

add_remove_owners.php

<?php

/** 
 * Removes user as owner if they are currently owner.
 */ 
function bglib_remove_owner($nid, $uid) {
  $u = user_load($uid);        
  $wrapper =  entity_metadata_wrapper('node', $nid);
  $owners = $wrapper->field_owners->value();
  foreach($owners as $delta => $owner) {
    if($owner == $u) {         
      unset($wrapper->field_owners[$delta]);
      $wrapper->save();        
    }
  } 
}   
    
/** 
 * Adds user as owner if they are not already
 */ 
function bglib_add_owner($nid, $uid) {
  $found = false;
  $u = user_load($uid);        
  $wrapper =  entity_metadata_wrapper('node', $nid);
  $owners = $wrapper->field_owners->value();
  foreach($owners as $owner) { 
    if ($owner == $u) {        
      $found = true;           
    }
  } 
  if($found == false) {
    $wrapper->field_owners[] = $u;
    $wrapper->save();
  }
}

emw_with_lists.php

<?php 

$node_wrapper = entity_metadata_wrapper('node', 8);
$owners = $node_wrapper->field_owners->value();

$u = user_load(1);
print "owners are : " ;
$found = 0;
foreach($owners as $delta => $owner) {
  print "\n owner name: " . $owner->name;
  if($u == $owner) {
    print "\nfound owner at $delta!";
    $found = $delta;
    unset($node_wrapper->field_owners[$delta]);
    $node_wrapper->save();
  }
  //dpm( $owner);
}
dpm($owners);

//dpm($node_wrapper->field_owners);